A couple questions... first off, is it my imagination, or do the ground spawns (mushrooms, butterflies, etc) become more and more common the longer you leave a particular village active and open?

Second, how in the world do you get the beetles to start spawning? I have level two exploration, which SEEMS to indicate that we should start getting beetles, but I'm still only getting pebbles, shells and butterflies.

The beetles might be in an undiscovered part of the village.
Think about where bugs and beetles like to hide.

Getting beetles requires you to complete one of the puzzles and the collectibles appear at totally random times. It makes no difference how long the game has been running. The only difference is obviously common items are going to appear more often than rare ones.